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ilk_bibliography <- tar_read(ias_bibliography)Quality report of the IPBES IAS bibliography
Introduction
This report assesses the following in regards to the provided bibliography named bibliography_metrics.rds:
Remarks: - Group ID is in the json, but not in the csv. The group ID makes it possible to directly jump to the reference in the Zotero Library online.
Bibliography Setup
The bibliography is loaded and the DOIs, ISBNs and ISSNs are extracted. In a second step, the corresponding works are downloaded from [OpenAlex(https://openalex.org)].
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bibliography <- tar_read(ias_bibliography)Data Quality of the Bibliography
Cleanliness of bibliography
One measure of the cleanliness of a Bibliography is assessed by checking the number of references that have a DOI. The following table gives an overview over some numbers regarding the DOIs, ISBNs and ISSNs in the bibliography.
Entries with DOIs, ISBNs or ISSNs
To identify a reference, the most widely used identifier is the DOI. The following table shows the number of references with a DOI and the number of unique DOIs.
To consider duplicate ISBNs or ISSNs as duplicates entries in the library is not waranted as e.g. differenc chapters of a book can be separate entries in the library and therefore lead toi duplicates.
- DOIs: 3863 (73.8482126%) - 2 duplicates
- ISBNs: 453 (8.6599121%) - 57 duplicates
- ISSNs: 3301 (63.1045689%) - 2118 duplicates
The following DOIs are duplicates in the bibliography. This table should be empty.
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# duplicate_isbns <- paste0("https://isbnsearch.org/search?s=", bibliography$dois_bib[duplicated(bibliography$isbns)])
# duplicate_issns <- paste0("", bibliography$dois_bib[duplicated(bibliography$issns)])
data.frame(
Type = "doi",
Identifier = sprintf('<a href="https://doi.org/%s" target="_blank">%s</a>', bibliography$dois_bib[duplicated(bibliography$dois_bib)], bibliography$dois_bib[duplicated(bibliography$dois_bib)])
) |>
knitr::kable(
caption = "Duplicate DOIs in the Bibliography",
escape = FALSE
)| Type | Identifier |
|---|---|
| doi | 10.1111/emr.12464 |
| doi | 10.1111/mam.12277 |
DOIs in Open Alex
To validate the existence and validity of the DOIs, we check if the DOIs are in the OpenAlex database.
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dois_not_in_oa <- unique(bibliography$dois_bib)[!(unique(bibliography$dois_bib) %in% bibliography$dois_works)]
dois_valid <- dois_not_in_oa[IPBES.R::doi_valid(dois_not_in_oa)]Of the 3861 in the library which have a DOI, 471 (12.1989122%) are in not in OpenAlex.
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data.frame(
Type = "doi",
Identifier = sprintf('<a href="https://doi.org/%s" target="_blank">%s</a>', dois_not_in_oa, dois_not_in_oa)
) |>
IPBES.R::table_dt(caption = "The Caption")Of these 66 are not valid. These are:
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data.frame(
Type = "doi",
Identifier = sprintf('<a href="https://doi.org/%s" target="_blank">%s</a>', dois_not_in_oa[!(dois_not_in_oa %in% dois_valid)], dois_not_in_oa[!(dois_not_in_oa %in% dois_valid)])
) |>
knitr::kable(
caption = "Non Valid DOIs in the Bibliography",
escape = FALSE
)TODO Finally we check, if these dois exist but are not ingested into OpanAlex. This is done using the doi.org resolver This is disabled at the moment.
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dois_exist <- IPBES.R::doi_exists(
dois_valid,
cache_file = file.path(".", "cache", "doi_exist.rds")
)Show the code
to_check <- bibliography$dois_bib[!(bibliography$dois_bib %in% dois_works)]
dois_valid <- IPBES.R::doi_valid(bibliography$dois_bib)
dois_openalex <- bibliography$dois_bib %in% dois_works
names(dois_openalex) <- bibliography$dois_bib
dois_exist <- IPBES.R::doi_exists(to_check, cache_file = file.path(".", "cache", "doi_exist.rds"))
dois_not_retracted <- IPBES.R::doi_not_retracted(bibliography$dois_bib, cache_file = file.path(".", "cache", "doi_not_retracted.rds"))
sprintf(
fmt = paste(
"Number of references: \t\t %d",
"Number of DOIs: \t\t %d",
"Number of Duplicate DOIs: \t %d",
"Number of DOIs in OpenAlex: \t %d ( %f %)",
"Number of Existing DOIs: \t %d",
"Number of Retracted DOIs: \t %d",
"Percentage of Duplicate DOIs: \t %f",
sep = "\n"
),
nrow(bibliography),
sum(!is.na(bibliography$dois_bib)),
length(bibliography$dois_bib) - length(unique((bibliography$dois_bib))),
sum(dois_openalex), 100 * sum(dois_openalex) / nrow(bibliography),
sum(dois_exist),
sum(!dois_not_retracted),
((dois_valid |> unique() |> length()) / length(dois_valid)) |> round(digits = 3) * 100
) |> cat()Show the code
oldopts <- options(knitr.kable.NA = "")
data.frame(
Measure = c(
"# References",
"**DOI**",
"# DOIs",
"# Duplicate DOIs",
"# Existing DOIs",
"# Retracted DOIs",
"% Duplicate DOIs",
"**ISBN**",
"# ISBNs",
"# Duplicate ISBNs",
"**ISSN**",
"# ISSNs",
"# Duplicate ISSNs"
),
Value = c(
nrow(bibliography),
NA,
sum(!is.na(bibliography$dois_bib)),
length(bibliography$dois_bib) - length(unique((bibliography$dois_bib))),
sum(dois_exist),
sum(!dois_not_retracted),
((dois_valid |> unique() |> length()) / length(dois_valid)) |> round(digits = 3) * 100,
NA,
sum(!is.na(bibliography$isbns)),
length(bibliography$isbns) - length(unique((bibliography$isbns))),
NA,
sum(!is.na(bibliography$issns)),
length(bibliography$issns) - length(unique((bibliography$issns)))
)
) |>
knitr::kable(
caption = "Cleanliness of the Bibliography",
)
options(oldopts)Contentual and Bibliographic analysis
Publication types
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bibliography$bibliography |>
dplyr::group_by(
Item.Type
) |>
dplyr::summarize(
count = n()
) |>
dplyr::arrange(
desc(count)
) |>
knitr::kable()| Item.Type | count |
|---|---|
| journalArticle | 4157 |
| bookSection | 305 |
| book | 244 |
| report | 236 |
| webpage | 97 |
| conferencePaper | 83 |
| document | 67 |
| thesis | 15 |
| dataset | 12 |
| blogPost | 9 |
| preprint | 2 |
| magazineArticle | 1 |
| newspaperArticle | 1 |
| presentation | 1 |
| videoRecording | 1 |
Year of Publication
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tar_read(plot_pub_year_ias)Warning: Removed 40 rows containing missing values or values outside the scale range
(`geom_line()`).Warning: Removed 196 rows containing missing values or values outside the scale range
(`geom_line()`).
Access Status of References
This is checked by using the OpenAlex retrieved works. Therefore it is li=mited to the works that are on OpenAlex. At the moment, only references with a DOI were retrieved from OpenAlex.
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tar_read(plot_oa_status_ias)
50 Most often cited Journals
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tar_read(plot_top_journals_ias)
This table contains all Journals as specified in the Zotero database.
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tar_read(plot_top_journals_data_ias) |>
IPBES.R::table_dt("cited_journals")VOSViewer Example
ILK References in Bibliography
This comparison is at the moment done using the DOIs in the target and the ILK bibliography. Entries which have no DOI can not be compared at the mopment. A comparison could be achieved by using text comparison of the title, but this is not implemenmted yet.
From the 3863 references in the target bibliography, 3863 (1%) are in the ILK bibliography (3863 references).